Been out of the loop for a few days or I would have replied to this earlier. Firstly to remind Kaz that his skewed opinion of blender is soley based on a small error in the export function of a bizzare outdated format that was fixed the version later and has been fixed for the past 6 years or so, and I'd also like to point out that PCS1 produced faulty collision detection data long after the DXF export error was fixed anyway.

As for the export method, Warp Shadow's will work, but there is now a COB-export python script modified by Water that saves a COB that can be directly converted to POF using PCS2. It can't correctly export hierarchy, but it does keep the objects correctly separate. This means we can bypass truecrap and all the pain, misery and instabilities it brings and just do the hierarchy in PCS2. All the cobs I've converted using this method have been 100% stable collision mesh data-wise as far as I've been able to tell.
The one thing you might have a bit of trouble with is that before export, you need to apply the scaling and rotation (ctrl+A) that has been applied to the objects in the ship or they will return to their original size and orientation during export.
The python file is here:
http://www.sectorgame.com/ti-file-dump/VasudanAdmiral/truespace_FS2_basic-export.pyPut it in your "<blender install directory>\.blender\scripts" folder and it will add "Truespace Basic -FS2- (.cob)" to your export list.
If for whatever reason you absolutely need to get your ship into truecrap before conversion, the best way to do it is either directly open the cob the script exports, or use the Direct X format (.X) and save it as a cob using 3d exploration. This method retains everything but the hierarchy.